Forget about the second order effects. The reason the extra instructions in first approximation do not matter is that loops typically are limited by carried loop dependencies.
Think about this: a machine with infinite execution units and memory bandwidth, potentially could execute all iterations of a loop at the same time, in parallel.
Unless each loop iteration depends somehow on the result of the previous iteration. Then only independent instructions of that iteration can execute in parallel and the loop is latency-chain bound (especially when it involves memory accesses). This is often the case. Because branch prediction breaks dependencies, bound checking is never part of a dependency chain, so it is often free or nearly so. For more optimized code, the assumption of infinite resources is of course not warranted and execution bandwidth and possibly even memory bandwidth need to be taken into consideration.
Think about this: a machine with infinite execution units and memory bandwidth, potentially could execute all iterations of a loop at the same time, in parallel.
Unless each loop iteration depends somehow on the result of the previous iteration. Then only independent instructions of that iteration can execute in parallel and the loop is latency-chain bound (especially when it involves memory accesses). This is often the case. Because branch prediction breaks dependencies, bound checking is never part of a dependency chain, so it is often free or nearly so. For more optimized code, the assumption of infinite resources is of course not warranted and execution bandwidth and possibly even memory bandwidth need to be taken into consideration.